On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
Hi,
As far as I understand, a topology (a .top file) and a conformation
(e.g., a .gro file) contain enough information to calculate the
torsion angles of that specific conformation.
Table 5.5 (page 124) in the GROMACS manual[1] describes possible
interactions (which are contained in the topology) between different
molecules while the conformation contains the cartesian coordinates. I
did not immediately find a way to convert between the cartesian
coordinates and the torsion angles. Can GROMACS do it or do I need to
understand (or just find) all the functions/formulas that are
referenced in Table 5.5?
Section 4.2 has the relevant definitions. Table 5.5 pertains to the
definition of force field elements that act upon (for example) such
internal coordinates, which is not what you're looking for.
I have included screenshots of Table 5.5[2] and the relevant part of
some example .top file[3].
(Also, it seems that I can use the read_tpx method defined in
include/tpxio.h to read in a topology from a .tpr file. This would
then, after converting the cartesian coordinates of some conformation,
enable me to work with the torsion angles in my own program before
writing cartesian coordinates back for use with GROMACS.)
Either
a) write something that post-processes the result of grompp -pp in
concert with the same coordinate file to get the internal coordinates, or
b) use a hacked version of mdrun that writes internal coordinates from
within src/gmxlib/bondfree.c (probably used as mdrun -rerun)
to create input for your procedure.
Mark
Regards,
Martin.
[1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf
[2]
http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png
<http://imada.sdu.dk/%7Emkjens04/gromacs/intra-molecular_interactions_definitions.png>
[3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png
<http://imada.sdu.dk/%7Emkjens04/gromacs/part_of_top_file.png>
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